SO, do prone and cover stack? They both provide untyped bonuses to AC and I don't see anywhere where the book says they don't so I think RAW is does, though I personally don't think that it is intended to work that way.
Can anyone point out where they do not stack? Are there specific instances when it would and when it wouldn't?
For instance I can see you being prone behind your buddy, you gain +4 from prone and +4 from soft cover for a total of +8 (ridiculously high bonus).
Page 266
"Bonuses that do not list a bonus type do stack, both with each other and with all typed bonuses. Such bonuses, often referred to as “untyped” bonuses, are among the most utilitarian of all bonuses in the game."
Untyped bonuses always stack with each other and bonuses of any other type.
Now having said that, if are lying on the ground with a sniper rifle that is slotted into a metal firing shield (or something) then yeah you deserve to have those bonuses stack...but you're also lying on the ground with an unwieldy weapon when the enemies decide to start grenading and rocketing the bejeebus out of the area :)
Here's a thing though. Cover gives you a reflex save bonus. Being Prone doesn't give you a reflex save penalty. So the sniper is pretty decently protected against grenades and other AOE.
The only real downside is the lack of mobility and having some assault person rush in to melee range.
Being prone behind cover will often turn it into total cover. Which is great, since you can't be hit at all, except you also can't shoot from total cover.
GM call if that is the case.